Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities. More...
#include <OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMeanIterative.h>
Public Types | |
| enum | IntensityThresholdCalculation { MANUAL = -1, AUTOMAXBYSTDEV = 0, AUTOMAXBYPERCENT = 1 } |
| method to use for estimating the maximal intensity that is used for histogram calculation More... | |
| typedef SignalToNoiseEstimator< Container >::PeakIterator | PeakIterator |
| typedef SignalToNoiseEstimator< Container >::PeakType | PeakType |
| typedef SignalToNoiseEstimator< Container >::GaussianEstimate | GaussianEstimate |
 Public Types inherited from SignalToNoiseEstimator< Container > | |
| typedef Container::const_iterator | PeakIterator |
| typedef PeakIterator::value_type | PeakType |
| Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } |
| Possible log types. More... | |
Public Member Functions | |
| SignalToNoiseEstimatorMeanIterative () | |
| default constructor More... | |
| SignalToNoiseEstimatorMeanIterative (const SignalToNoiseEstimatorMeanIterative &source) | |
| Copy Constructor. More... | |
| virtual | ~SignalToNoiseEstimatorMeanIterative () |
| Destructor. More... | |
Assignment | |
| SignalToNoiseEstimatorMeanIterative & | operator= (const SignalToNoiseEstimatorMeanIterative &source) |
| Public Member Functions inherited from SignalToNoiseEstimator< Container > | |
| SignalToNoiseEstimator () | |
| Constructor. More... | |
| SignalToNoiseEstimator (const SignalToNoiseEstimator &source) | |
| Copy constructor. More... | |
| SignalToNoiseEstimator & | operator= (const SignalToNoiseEstimator &source) |
| Assignment operator. More... | |
| virtual | ~SignalToNoiseEstimator () |
| Destructor. More... | |
| virtual void | init (const PeakIterator &it_begin, const PeakIterator &it_end) |
| Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately. More... | |
| virtual void | init (const Container &c) |
| Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately. More... | |
| virtual double | getSignalToNoise (const PeakIterator &data_point) |
| virtual double | getSignalToNoise (const PeakType &data_point) |
| Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages. More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor. More... | |
| virtual | ~DefaultParamHandler () |
| Destructor. More... | |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More... | |
| void | setParameters (const Param ¶m) |
| Sets the parameters. More... | |
| const Param & | getParameters () const |
| Non-mutable access to the parameters. More... | |
| const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More... | |
| const String & | getName () const |
| Non-mutable access to the name. More... | |
| void | setName (const String &name) |
| Mutable access to the name. More... | |
| const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More... | |
| Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor. More... | |
| ~ProgressLogger () | |
| Destructor. More... | |
| ProgressLogger (const ProgressLogger &other) | |
| Copy constructor. More... | |
| ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More... | |
| void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More... | |
| LogType | getLogType () const |
| Returns the type of progress log being used. More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More... | |
| void | setProgress (SignedSize value) const |
| Sets the current progress. More... | |
| void | endProgress () const |
| Ends the progress display. More... | |
Protected Member Functions | |
| virtual void | computeSTN_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_) |
| void | updateMembers_ () |
| overridden function from DefaultParamHandler to keep members up to date, when a parameter is changed More... | |
| Protected Member Functions inherited from SignalToNoiseEstimator< Container > | |
| GaussianEstimate | estimate_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_) const |
| calculate mean & stdev of intensities of a spectrum More... | |
| Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
| double | max_intensity_ |
| maximal intensity considered during binning (values above get discarded) More... | |
| double | auto_max_stdev_Factor_ |
| parameter for initial automatic estimation of "max_intensity_": a stdev multiplier More... | |
| double | auto_max_percentile_ |
| parameter for initial automatic estimation of "max_intensity_" percentile or a stdev More... | |
| int | auto_mode_ |
| determines which method shall be used for estimating "max_intensity_". valid are MANUAL=-1, AUTOMAXBYSTDEV=0 or AUTOMAXBYPERCENT=1 More... | |
| double | win_len_ |
| range of data points which belong to a window in Thomson More... | |
| int | bin_count_ |
| number of bins in the histogram More... | |
| double | stdev_ |
| multiplier for the stdev of intensities More... | |
| int | min_required_elements_ |
| minimal number of elements a window needs to cover to be used More... | |
| double | noise_for_empty_window_ |
| Protected Attributes inherited from SignalToNoiseEstimator< Container > | |
| std::map< PeakType, double, typename PeakType::PositionLess > | stn_estimates_ |
| stores the noise estimate for each peak More... | |
| PeakIterator | first_ |
| points to the first raw data point in the interval More... | |
| PeakIterator | last_ |
| points to the right position next to the last raw data point in the interval More... | |
| bool | is_result_valid_ |
| flag: set to true if SignalToNoise estimates are calculated and none of the params were changed. otherwise false. More... | |
| Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ |
| Container for current parameters. More... | |
| Param | defaults_ |
| Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
| std::vector< String > | subsections_ |
| Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
| String | error_name_ |
| Name that is displayed in error messages during the parameter checking. More... | |
| bool | check_defaults_ |
| If this member is set to false no checking if parameters in done;. More... | |
| bool | warn_empty_defaults_ |
| If this member is set to false no warning is emitted when defaults are empty;. More... | |
| Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| time_t | last_invoke_ |
| ProgressLoggerImpl * | current_logger_ |
Additional Inherited Members | |
| Static Protected Member Functions inherited from ProgressLogger | |
| static String | logTypeToFactoryName_ (LogType type) |
| Return the name of the factory product used for this log type. More... | |
| Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
Detailed Description
template<typename Container = MSSpectrum>
class OpenMS::SignalToNoiseEstimatorMeanIterative< Container >
Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme which discards high intensities.
For each datapoint in the given scan, we collect a range of data points around it (param: win_len). The noise for a datapoint is estimated iteratively by discarding peaks which are more than (stdev_mp * StDev) above the mean value. After three iterations, the mean value is considered to be the noise level. If the number of elements in the current window is not sufficient (param: min_required_elements), the noise level is set to a default value (param: noise_for_empty_window).
The whole computation is histogram based, so the user will need to supply a number of bins (param: bin_count), which determines the level of error and runtime. The maximal intensity for a datapoint to be included in the histogram can be either determined automatically (param: auto_mode) by two different methods or can be set directly by the user (param: max_intensity).
Changing any of the parameters will invalidate the S/N values (which will invoke a recomputation on the next request).
- Note
- If more than 20 percent of windows have less than min_required_elements of elements, a warning is issued to stderr and noise estimates in those windows are set to the constant noise_for_empty_window.
| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| max_intensity | int | -1 | min: -1 | maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). |
| auto_max_stdev_factor | float | 3 | min: 0 max: 999 | parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev |
| auto_max_percentile | int | 95 | min: 0 max: 100 | parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile |
| auto_mode | int | 0 | min: -1 max: 1 | method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method |
| win_len | float | 200 | min: 1 | window length in Thomson |
| bin_count | int | 30 | min: 3 | number of bins for intensity values |
| stdev_mp | float | 3 | min: 0.01 max: 999 | multiplier for stdev |
| min_required_elements | int | 10 | min: 1 | minimum number of elements required in a window (otherwise it is considered sparse) |
| noise_for_empty_window | float | 1e+20 | noise value used for sparse windows |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Member Typedef Documentation
◆ GaussianEstimate
| typedef SignalToNoiseEstimator<Container>::GaussianEstimate GaussianEstimate |
◆ PeakIterator
| typedef SignalToNoiseEstimator<Container>::PeakIterator PeakIterator |
◆ PeakType
| typedef SignalToNoiseEstimator<Container>::PeakType PeakType |
Member Enumeration Documentation
◆ IntensityThresholdCalculation
Constructor & Destructor Documentation
◆ SignalToNoiseEstimatorMeanIterative() [1/2]
|
inline |
default constructor
References DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), Param::setMaxFloat(), Param::setMaxInt(), Param::setMinFloat(), Param::setMinInt(), DefaultParamHandler::setName(), and Param::setValue().
◆ SignalToNoiseEstimatorMeanIterative() [2/2]
|
inline |
◆ ~SignalToNoiseEstimatorMeanIterative()
|
inlinevirtual |
Destructor.
Member Function Documentation
◆ computeSTN_()
|
inlineprotectedvirtual |
calculate StN values for all datapoints given, by using a sliding window approach
- Parameters
-
scan_first_ first element in the scan scan_last_ last element in the scan (disregarded)
- Exceptions
-
Throws Exception::InvalidValue
Implements SignalToNoiseEstimator< Container >.
References SignalToNoiseEstimatorMeanIterative< Container >::auto_max_percentile_, SignalToNoiseEstimatorMeanIterative< Container >::auto_max_stdev_Factor_, SignalToNoiseEstimatorMeanIterative< Container >::auto_mode_, SignalToNoiseEstimatorMeanIterative< Container >::AUTOMAXBYPERCENT, SignalToNoiseEstimatorMeanIterative< Container >::AUTOMAXBYSTDEV, SignalToNoiseEstimatorMeanIterative< Container >::bin_count_, ProgressLogger::endProgress(), SignalToNoiseEstimator< Container >::estimate_(), SignalToNoiseEstimatorMeanIterative< Container >::max_intensity_, SignalToNoiseEstimator< Container >::GaussianEstimate::mean, SignalToNoiseEstimatorMeanIterative< Container >::min_required_elements_, SignalToNoiseEstimatorMeanIterative< Container >::noise_for_empty_window_, ProgressLogger::setProgress(), ProgressLogger::startProgress(), SignalToNoiseEstimatorMeanIterative< Container >::stdev_, SignalToNoiseEstimator< Container >::stn_estimates_, SignalToNoiseEstimator< Container >::GaussianEstimate::variance, and SignalToNoiseEstimatorMeanIterative< Container >::win_len_.
◆ operator=()
|
inline |
◆ updateMembers_()
|
inlineprotectedvirtual |
overridden function from DefaultParamHandler to keep members up to date, when a parameter is changed
Reimplemented from DefaultParamHandler.
References SignalToNoiseEstimatorMeanIterative< Container >::auto_max_percentile_, SignalToNoiseEstimatorMeanIterative< Container >::auto_max_stdev_Factor_, SignalToNoiseEstimatorMeanIterative< Container >::auto_mode_, SignalToNoiseEstimatorMeanIterative< Container >::bin_count_, Param::getValue(), SignalToNoiseEstimator< Container >::is_result_valid_, SignalToNoiseEstimatorMeanIterative< Container >::max_intensity_, SignalToNoiseEstimatorMeanIterative< Container >::min_required_elements_, SignalToNoiseEstimatorMeanIterative< Container >::noise_for_empty_window_, DefaultParamHandler::param_, SignalToNoiseEstimatorMeanIterative< Container >::stdev_, and SignalToNoiseEstimatorMeanIterative< Container >::win_len_.
Referenced by SignalToNoiseEstimatorMeanIterative< Container >::SignalToNoiseEstimatorMeanIterative().
Member Data Documentation
◆ auto_max_percentile_
|
protected |
parameter for initial automatic estimation of "max_intensity_" percentile or a stdev
Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().
◆ auto_max_stdev_Factor_
|
protected |
parameter for initial automatic estimation of "max_intensity_": a stdev multiplier
Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().
◆ auto_mode_
|
protected |
determines which method shall be used for estimating "max_intensity_". valid are MANUAL=-1, AUTOMAXBYSTDEV=0 or AUTOMAXBYPERCENT=1
Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().
◆ bin_count_
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protected |
number of bins in the histogram
Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().
◆ max_intensity_
|
protected |
maximal intensity considered during binning (values above get discarded)
Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().
◆ min_required_elements_
|
protected |
minimal number of elements a window needs to cover to be used
Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().
◆ noise_for_empty_window_
|
protected |
used as noise value for windows which cover less than "min_required_elements_" use a very high value if you want to get a low S/N result
Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().
◆ stdev_
|
protected |
multiplier for the stdev of intensities
Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().
◆ win_len_
|
protected |
range of data points which belong to a window in Thomson
Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().